Showing : normalization • reset
0
votes
1
reply
1.3k
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
1
reply
767
views
processing samples with significantly different counts
DESeq2 Normalization
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
5
replies
2.3k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
2
votes
3
replies
1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
3
votes
3
replies
1.3k
views
What is cpmByGroup used for?
edgeR Normalization
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
2
replies
1.4k
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
2.9 years ago rcreswell01 • 0
1
vote
1
reply
1.3k
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
6
votes
2
replies
4.3k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
2
replies
3.0k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 20 months ago by • 0 • written 3.0 years ago by ▴ 10
4
votes
8
replies
4.6k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 18 months ago by • 0 • written 3.0 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
3.0 years ago Arend ▴ 10
0
votes
0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.0 years ago Zhijie • 0
1
vote
0
replies
1.4k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
3.0 years ago r_grau ▴ 10
3
votes
4
replies
3.2k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.1 years ago • updated 3.0 years ago spg • 0
4
votes
8
replies
3.5k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.6 years ago by 53k • written 3.1 years ago by ▴ 20
0
votes
1
reply
1.2k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
votes
2
replies
1.6k
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
2
votes
4
replies
6.0k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
2
replies
1.4k
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
3.1 years ago Sally • 0
1
vote
2
replies
1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.1 years ago mohammedtoufiq91 ▴ 10
3
votes
6
replies
3.5k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.2 years ago • updated 3.1 years ago Sara • 0
0
votes
2
replies
1.2k
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
3.2 years ago michela ▴ 20
2
votes
4
replies
4.0k
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 20
1
vote
2
replies
5.5k
views
Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 3.3 years ago by ▴ 10 • written 3.3 years ago by • 0
0
votes
1
reply
946
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
0
votes
5
replies
2.5k
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 7 months ago by 43k • written 3.4 years ago by • 0
2
votes
2
replies
7.9k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 3.4 years ago by ▴ 200 • written 13.0 years ago by ▴ 450
0
votes
1
reply
1.9k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
1
vote
1
reply
1.4k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
2
votes
4
replies
2.8k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.5 years ago Yang Shi ▴ 10
4
votes
3
replies
3.2k
views
Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
3.6 years ago Karla ▴ 10
0
votes
0
replies
644
views
Seek for ideas on model-based normalization
Norm Normalization
3.6 years ago jinghuazhao • 0
2
votes
7
replies
2.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.6 years ago Jess • 0
3
votes
3
replies
2.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 10
1
vote
1
reply
2.2k
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 3.6 years ago by 53k • written 3.7 years ago by • 0
2
votes
3
replies
1.7k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.7 years ago • updated 3.6 years ago bers.anthrope ▴ 10
1
vote
5
replies
13k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Should I keep libsizes?
Normalization edgeR
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
0
votes
2
replies
4.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.4 years ago by • 0 • written 3.8 years ago by • 0
0
votes
1
reply
2.0k
views
Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.8 years ago by 53k • written 16.9 years ago by ▴ 30
0
votes
0
replies
916
views
Using geNetClassifier with RNA seq data
geNetClassifier Normalization
3.8 years ago nhaus ▴ 70
1
vote
1
reply
3.0k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.8 years ago by ▴ 760 • written 3.8 years ago by • 0
3
votes
4
replies
2.6k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
3
votes
3
replies
2.5k
views
Deseq2 normalization steps
deseq2 normalization
updated 3.9 years ago by 43k • written 6.6 years ago by • 0
1
vote
7
replies
10k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.8 years ago by • 0 • written 7.0 years ago by ▴ 10
3
votes
5
replies
4.9k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
4
votes
4
replies
3.6k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 2.1 years ago by 53k • written 4.1 years ago by ▴ 10
1,761 results • Page 2 of 36
Recent ...
Replies
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Votes
Answer: Where do the filename come from in the LOLA datasets?
Bioconductor Maintainer Application
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Teacher to Michael Love 43k
Locations • All
The city by the bay, 9 minutes ago
The Netherlands, 2 hours ago
WEHI, Melbourne, Australia, 2 hours ago
United States, 3 hours ago
Barcelona, Spain, 6 hours ago
Traffic: 1023 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6